Home LiteratureArticle Details
PMID: 15214846 Published · ppublish English Journal Article Review

Carbohydrate-binding modules: fine-tuning polysaccharide recognition.

The Biochemical journal ·Vol. 382 ·No. Pt 3 ·2004-09-15 ·Pages 769-81

Boraston AB, Bolam DN, Gilbert HJ, Davies GJ

Abstract

The enzymic degradation of insoluble polysaccharides is one of the most important reactions on earth. Despite this, glycoside hydrolases attack such polysaccharides relatively inefficiently as their target glycosidic bonds are often inaccessible to the active site of the appropriate enzymes. In order to overcome these problems, many of the glycoside hydrolases that utilize insoluble substrates are modular, comprising catalytic modules appended to one or more non-catalytic CBMs (carbohydrate-binding modules). CBMs promote the association of the enzyme with the substrate. In view of the central role that CBMs play in the enzymic hydrolysis of plant structural and storage polysaccharides, the ligand specificity displayed by these protein modules and the mechanism by which they recognize their target carbohydrates have received considerable attention since their discovery almost 20 years ago. In the last few years, CBM research has harnessed structural, functional and bioinformatic approaches to elucidate the molecular determinants that drive CBM-carbohydrate recognition. The present review summarizes the impact structural biology has had on our understanding of the mechanisms by which CBMs bind to their target ligands.

MeSH Terms
Binding Sites Carrier Proteins/chemistry,metabolism Glycoside Hydrolases/chemistry Ligands Models, Molecular Polysaccharides/metabolism Protein Structure, Secondary Protein Structure, Tertiary
Chemicals
Carrier Proteins Ligands Polysaccharides Glycoside Hydrolases
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Boraston Alisdair B
Biochemistry and Microbiology, University of Victoria, PO Box 3055 STN CSC, Victoria, BC, Canada V8W 3P6.
Bolam David N
Gilbert Harry J
Davies Gideon J
References (82)
82 references, click to expand
  1. Precise excision of the cellulose binding domains from two Cellulomonas fimi cellulases by a homologous protease and the effect on catalysis.
    J Biol Chem. 1988 Jul 25;263(21):10401-7 PMID: 3134347
  2. Importance of the carbohydrate-binding module of Clostridium stercorarium Xyn10B to xylan hydrolysis.
    Biosci Biotechnol Biochem. 2001 Jan;65(1):41-7 PMID: 11272844
  3. High-resolution crystal structures of the lectin-like xylan binding domain from Streptomyces lividans xylanase 10A with bound substrates reveal a novel mode of xylan binding.
    Biochemistry. 2002 Apr 2;41(13):4246-54 PMID: 11914070
  4. The binding pattern of two carbohydrate-binding modules of laminarinase Lam16A from Thermotoga neapolitana: differences in beta-glucan binding within family CBM4.
    Microbiology. 2001 Mar;147(Pt 3):621-9 PMID: 11238969
  5. Both binding sites of the starch-binding domain of Aspergillus niger glucoamylase are essential for inducing a conformational change in amylose.
    J Mol Biol. 2001 Nov 9;313(5):1149-59 PMID: 11700070
  6. Chitin-binding proteins in invertebrates and plants comprise a common chitin-binding structural motif.
    J Biol Chem. 2000 Jun 16;275(24):17929-32 PMID: 10770921
  7. Glycoside hydrolase carbohydrate-binding modules as molecular probes for the analysis of plant cell wall polymers.
    Anal Biochem. 2004 Mar 1;326(1):49-54 PMID: 14769335
  8. Evidence for the extended helical nature of polysaccharide epitopes. The 2.8 A resolution structure and thermodynamics of ligand binding of an antigen binding fragment specific for alpha-(2-->8)-polysialic acid.
    Biochemistry. 1995 May 23;34(20):6737-44 PMID: 7538787
  9. C1-Cx revisited: intramolecular synergism in a cellulase.
    Proc Natl Acad Sci U S A. 1994 Nov 22;91(24):11383-7 PMID: 7972069
  10. Identification of novel beta-mannan- and beta-glucan-binding modules: evidence for a superfamily of carbohydrate-binding modules.
    Biochem J. 2001 Jun 15;356(Pt 3):791-8 PMID: 11389686
  11. Ab initio structure determination and functional characterization of CBM36; a new family of calcium-dependent carbohydrate binding modules.
    Structure. 2004 Jul;12(7):1177-87 PMID: 15242594
  12. The structure of barley alpha-amylase isozyme 1 reveals a novel role of domain C in substrate recognition and binding: a pair of sugar tongs.
    Structure. 2003 Aug;11(8):973-84 PMID: 12906828
  13. Nucleotide sequence and X-ray structure of cyclodextrin glycosyltransferase from Bacillus circulans strain 251 in a maltose-dependent crystal form.
    J Mol Biol. 1994 Feb 18;236(2):590-600 PMID: 8107143
  14. All three surface tryptophans in Type IIa cellulose binding domains play a pivotal role in binding both soluble and insoluble ligands.
    FEBS Lett. 1998 Jun 16;429(3):312-6 PMID: 9662439
  15. Evidence for synergy between family 2b carbohydrate binding modules in Cellulomonas fimi xylanase 11A.
    Biochemistry. 2001 Feb 27;40(8):2468-77 PMID: 11327868
  16. Thermodynamics of ligand binding to the starch-binding domain of glucoamylase from Aspergillus niger.
    Eur J Biochem. 1994 Oct 1;225(1):133-41 PMID: 7925430
  17. X4 modules represent a new family of carbohydrate-binding modules that display novel properties.
    J Biol Chem. 2004 May 28;279(22):22953-63 PMID: 15004012
  18. The anatomy and taxonomy of protein structure.
    Adv Protein Chem. 1981;34:167-339 PMID: 7020376
  19. Glycoside hydrolases and glycosyltransferases. Families, modules, and implications for genomics.
    Plant Physiol. 2000 Dec;124(4):1515-9 PMID: 11115868
  20. Structural determinants of Ricinus communis agglutinin and toxin specificity for oligosaccharides.
    J Biol Chem. 1979 Oct 10;254(19):9795-9 PMID: 489569
  21. The binding specificity and affinity determinants of family 1 and family 3 cellulose binding modules.
    Proc Natl Acad Sci U S A. 2003 Jan 21;100(2):484-9 PMID: 12522267
  22. Solution structure of the granular starch binding domain of Aspergillus niger glucoamylase bound to beta-cyclodextrin.
    Structure. 1997 May 15;5(5):647-61 PMID: 9195884
  23. Recognition and hydrolysis of noncrystalline cellulose.
    J Biol Chem. 2003 Feb 21;278(8):6120-7 PMID: 12427734
  24. Molecular recognition of oligosaccharide epitopes by a monoclonal Fab specific for Shigella flexneri Y lipopolysaccharide: X-ray structures and thermodynamics.
    Biochemistry. 2002 Nov 19;41(46):13575-86 PMID: 12427018
  25. Cellulose-binding domains promote hydrolysis of different sites on crystalline cellulose.
    Proc Natl Acad Sci U S A. 2000 Sep 12;97(19):10342-7 PMID: 10962023
  26. Characterization and affinity applications of cellulose-binding domains.
    J Chromatogr B Biomed Sci Appl. 1998 Sep 11;715(1):283-96 PMID: 9792516
  27. The X6 "thermostabilizing" domains of xylanases are carbohydrate-binding modules: structure and biochemistry of the Clostridium thermocellum X6b domain.
    Biochemistry. 2000 May 2;39(17):5013-21 PMID: 10819965
  28. Surface diffusion of cellulases and their isolated binding domains on cellulose.
    J Biol Chem. 1997 Sep 19;272(38):24016-23 PMID: 9295354
  29. Co-operative binding of triplicate carbohydrate-binding modules from a thermophilic xylanase.
    Mol Microbiol. 2002 Jan;43(1):187-94 PMID: 11849546
  30. beta-Trefoil fold. Patterns of structure and sequence in the Kunitz inhibitors interleukins-1 beta and 1 alpha and fibroblast growth factors.
    J Mol Biol. 1992 Jan 20;223(2):531-43 PMID: 1738162
  31. Function of conserved tryptophans in the Aspergillus niger glucoamylase 1 starch binding domain.
    Biochemistry. 1997 Jun 17;36(24):7535-9 PMID: 9200704
  32. Glucoamylase starch-binding domain of Aspergillus niger B1: molecular cloning and functional characterization.
    Biochem J. 2003 Jun 15;372(Pt 3):905-10 PMID: 12646045
  33. The starch-binding domain from glucoamylase disrupts the structure of starch.
    FEBS Lett. 1999 Mar 19;447(1):58-60 PMID: 10218582
  34. Site-specific characterization of the association of xylooligosaccharides with the CBM13 lectin-like xylan binding domain from Streptomyces lividans xylanase 10A by NMR spectroscopy.
    Biochemistry. 2002 Apr 2;41(13):4255-63 PMID: 11914071
  35. Solution structure of the granular starch binding domain of glucoamylase from Aspergillus niger by nuclear magnetic resonance spectroscopy.
    J Mol Biol. 1996 Jun 28;259(5):970-87 PMID: 8683599
  36. Crystal structures of the sugar complexes of Streptomyces olivaceoviridis E-86 xylanase: sugar binding structure of the family 13 carbohydrate binding module.
    J Mol Biol. 2002 Feb 8;316(1):65-78 PMID: 11829503
  37. The crystal structure of the family 6 carbohydrate binding module from Cellvibrio mixtus endoglucanase 5a in complex with oligosaccharides reveals two distinct binding sites with different ligand specificities.
    J Biol Chem. 2004 May 14;279(20):21560-8 PMID: 15010454
  38. Determination of the three-dimensional solution structure of the C-terminal domain of cellobiohydrolase I from Trichoderma reesei. A study using nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing.
    Biochemistry. 1989 Sep 5;28(18):7241-57 PMID: 2554967
  39. Solution structure of the cellulose-binding domain of the endoglucanase Z secreted by Erwinia chrysanthemi.
    Biochemistry. 1997 Dec 23;36(51):16074-86 PMID: 9405041
  40. Crystal structure of a bacterial family-III cellulose-binding domain: a general mechanism for attachment to cellulose.
    EMBO J. 1996 Nov 1;15(21):5739-51 PMID: 8918451
  41. Promiscuity in ligand-binding: The three-dimensional structure of a Piromyces carbohydrate-binding module, CBM29-2, in complex with cello- and mannohexaose.
    Proc Natl Acad Sci U S A. 2002 Oct 29;99(22):14077-82 PMID: 12391332
  42. The location of the ligand-binding site of carbohydrate-binding modules that have evolved from a common sequence is not conserved.
    J Biol Chem. 2001 Dec 21;276(51):48580-7 PMID: 11673472
  43. Solution structure of the CBM10 cellulose binding module from Pseudomonas xylanase A.
    Biochemistry. 2000 Feb 8;39(5):978-84 PMID: 10653641
  44. Structural bases of lectin-carbohydrate affinities: comparison with protein-folding energetics.
    Protein Sci. 1999 May;8(5):1075-86 PMID: 10338018
  45. Studies of the cellulolytic system of Trichoderma reesei QM 9414. Analysis of domain function in two cellobiohydrolases by limited proteolysis.
    Eur J Biochem. 1988 Jan 4;170(3):575-81 PMID: 3338453
  46. A novel mechanism of xylan binding by a lectin-like module from Streptomyces lividans xylanase 10A.
    Biochem J. 2000 Sep 15;350 Pt 3:933-41 PMID: 10970811
  47. X-ray structure of Novamyl, the five-domain "maltogenic" alpha-amylase from Bacillus stearothermophilus: maltose and acarbose complexes at 1.7A resolution.
    Biochemistry. 1999 Jun 29;38(26):8385-92 PMID: 10387084
  48. Structure of raw starch-digesting Bacillus cereus beta-amylase complexed with maltose.
    Biochemistry. 1999 Jun 1;38(22):7050-61 PMID: 10353816
  49. Structural and thermodynamic dissection of specific mannan recognition by a carbohydrate binding module, TmCBM27.
    Structure. 2003 Jun;11(6):665-75 PMID: 12791255
  50. Structure and mechanism of endo/exocellulase E4 from Thermomonospora fusca.
    Nat Struct Biol. 1997 Oct;4(10):810-8 PMID: 9334746
  51. Crystal structure of Urtica dioica agglutinin, a superantigen presented by MHC molecules of class I and class II.
    Structure. 2000 Jun 15;8(6):593-603 PMID: 10873861
  52. Structure and ligand binding of carbohydrate-binding module CsCBM6-3 reveals similarities with fucose-specific lectins and "galactose-binding" domains.
    J Mol Biol. 2003 Mar 28;327(3):659-69 PMID: 12634060
  53. Crystal structure of the complex of porcine trypsin with soybean trypsin inhibitor (Kunitz) at 2.6-A resolution.
    Biochemistry. 1974 Sep 24;13(20):4212-28 PMID: 4472048
  54. Protein structure comparison by alignment of distance matrices.
    J Mol Biol. 1993 Sep 5;233(1):123-38 PMID: 8377180
  55. Essential role of the family-22 carbohydrate-binding modules for beta-1,3-1,4-glucanase activity of Clostridium stercorarium Xyn10B.
    FEBS Lett. 2004 Mar 12;561(1-3):155-8 PMID: 15013768
  56. Carbohydrate-binding proteins: tertiary structures and protein-sugar interactions.
    Annu Rev Biochem. 1986;55:287-315 PMID: 3527044
  57. Solution structure of a cellulose-binding domain from Cellulomonas fimi by nuclear magnetic resonance spectroscopy.
    Biochemistry. 1995 May 30;34(21):6993-7009 PMID: 7766609
  58. Binding site analysis of cellulose binding domain CBD(N1) from endoglucanse C of Cellulomonas fimi by site-directed mutagenesis.
    Biochemistry. 2000 Aug 1;39(30):8844-52 PMID: 10913296
  59. Binding specificity and thermodynamics of a family 9 carbohydrate-binding module from Thermotoga maritima xylanase 10A.
    Biochemistry. 2001 May 29;40(21):6240-7 PMID: 11371185
  60. A scheme for designating enzymes that hydrolyse the polysaccharides in the cell walls of plants.
    FEBS Lett. 1998 Mar 27;425(2):352-4 PMID: 9559678
  61. Crystal structures of the family 9 carbohydrate-binding module from Thermotoga maritima xylanase 10A in native and ligand-bound forms.
    Biochemistry. 2001 May 29;40(21):6248-56 PMID: 11371186
  62. Importance of hydrophobic and polar residues in ligand binding in the family 15 carbohydrate-binding module from Cellvibrio japonicus Xyn10C.
    Biochemistry. 2003 Aug 12;42(31):9316-23 PMID: 12899618
  63. Microcalorimetric study of wheat germ agglutinin binding to N-acetylglucosamine and its oligomers.
    Biochemistry. 1992 Dec 22;31(50):12624-8 PMID: 1472499
  64. Complex structures of Thermoactinomyces vulgaris R-47 alpha-amylase 1 with malto-oligosaccharides demonstrate the role of domain N acting as a starch-binding domain.
    J Mol Biol. 2004 Jan 16;335(3):811-22 PMID: 14687576
  65. Differential oligosaccharide recognition by evolutionarily-related beta-1,4 and beta-1,3 glucan-binding modules.
    J Mol Biol. 2002 Jun 21;319(5):1143-56 PMID: 12079353
  66. Clostridium thermocellum Xyn10B carbohydrate-binding module 22-2: the role of conserved amino acids in ligand binding.
    Biochemistry. 2001 Aug 7;40(31):9167-76 PMID: 11478884
  67. Recognition of cello-oligosaccharides by a family 17 carbohydrate-binding module: an X-ray crystallographic, thermodynamic and mutagenic study.
    J Mol Biol. 2001 Dec 7;314(4):797-806 PMID: 11733998
  68. Structure of ricin B-chain at 2.5 A resolution.
    Proteins. 1991;10(3):260-9 PMID: 1881882
  69. Analysis of binding of the family 2a carbohydrate-binding module from Cellulomonas fimi xylanase 10A to cellulose: specificity and identification of functionally important amino acid residues.
    Protein Eng. 2000 Nov;13(11):801-9 PMID: 11161112
  70. The three domains of a bacterial sialidase: a beta-propeller, an immunoglobulin module and a galactose-binding jelly-roll.
    Structure. 1995 Nov 15;3(11):1197-205 PMID: 8591030
  71. Pseudomonas cellulose-binding domains mediate their effects by increasing enzyme substrate proximity.
    Biochem J. 1998 May 1;331 ( Pt 3):775-81 PMID: 9560304
  72. The family 6 carbohydrate binding module CmCBM6-2 contains two ligand-binding sites with distinct specificities.
    J Biol Chem. 2004 May 14;279(20):21552-9 PMID: 15004011
  73. Structure of a family 15 carbohydrate-binding module in complex with xylopentaose. Evidence that xylan binds in an approximate 3-fold helical conformation.
    J Biol Chem. 2001 Dec 28;276(52):49061-5 PMID: 11598143
  74. Non-hydrolytic Disruption of Crystalline Structure of Cellulose by Cellulose Binding Domain and Linker Sequence of Cellobiohydrolase I from Penicillium janthinellum.
    Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai). 2001;33(1):13-18 PMID: 12053182
  75. Sugar tongs get a grip on the starch granule in barley alpha-amylase 1.
    Structure. 2003 Aug;11(8):903-4 PMID: 12906821
  76. An evolving hierarchical family classification for glycosyltransferases.
    J Mol Biol. 2003 Apr 25;328(2):307-17 PMID: 12691742
  77. Properties of a genetically reconstructed Prevotella ruminicola endoglucanase.
    Appl Environ Microbiol. 1992 Nov;58(11):3593-7 PMID: 1482181
  78. The structural basis for the ligand specificity of family 2 carbohydrate-binding modules.
    J Biol Chem. 2000 Dec 29;275(52):41137-42 PMID: 10973978
  79. Identification of a novel cellulose-binding domain within the multidomain 120 kDa xylanase XynA of the hyperthermophilic bacterium Thermotoga maritima.
    Mol Microbiol. 1995 Feb;15(3):431-44 PMID: 7783614
  80. The non-catalytic cellulose-binding domain of a novel cellulase from Pseudomonas fluorescens subsp. cellulosa is important for the efficient hydrolysis of Avicel.
    Biochem J. 1995 Aug 1;309 ( Pt 3):749-56 PMID: 7639689
  81. Enthalpic barriers to the hydrophobic binding of oligosaccharides to phage P22 tailspike protein.
    Biochemistry. 2001 May 1;40(17):5144-50 PMID: 11318636
  82. Binding of the cellulose-binding domain of exoglucanase Cex from Cellulomonas fimi to insoluble microcrystalline cellulose is entropically driven.
    Proc Natl Acad Sci U S A. 1996 Oct 29;93(22):12229-34 PMID: 8901562
Article Info
Journal
The Biochemical journal
Abbr.
Biochem J
ISSN
1470-8728
Published
2004-09-15
Pages
769-81
Language
English
Region
England
NLM ID
2984726R
PMCID
PMC1133952
Subset
IM
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com